Buschbeck-2017-Variants of core histones and t.pdf

One of the most abundant and most conserved pro-tein families in eukaryotic cells is the histone family.Histones package genetic information into the nuclear space and contribute to the regulation of all DNA template-based reactions.Core histones bindDNAas part of the nucleosome,the building block of chro-matin,and linker histones bind to DNA in the inter-nucleosomal space.Aside from the so-called canonical histones,which comprise the majority of any givenhis-tone species in any cell,evolution drove the emergence of histone variants,which endow chromatin with special properties in a locus-specific manner.With respect to the core histones,eight variants of H2A(H2A.X,H2A.Z.1,H2A.Z.2.1,H2A.Z.2.2,H2A Barr body defi-cient(H2A.Bbd;also known as H2A.B),macroH2A1.1,macroH2A1.2 and macroH2A2)and six variants of H3(H3.3,histone H3-like centromeric protein A(CENP-A),H3.1T,H3.5,H3.X(also known as H3.Y.2)and H3.Y(also known as H3.Y.1)have been identified in human somatic cells.In addition,two testis-specific variants of H2B(histone H2B type WT(H2BFWT;also known as H2B.W)and testis-specific histone H2B(TSH2B;also known as histone H2B type1A)have been found.However,no variants of H4 have yet been discovered in higher eukaryotes1.Surprisingly,in lower eukaryotes such as trypanosomes2 and some urochordates3,H4 variants have been found,which sug-gests either that functional specialization of this histone family is evolutionarily possible or that these variants do exist in higher eukaryotes but their detection has so far been unsuccessful.Notably,the different variants are distinct and unique in terms of their gene and protein sequences,as well as the timing of their transcription,how their RNA is processed and when they are depos-ited on DNA during the cell cycle(FIG.1).The canonical histones are deposited on DNA during replication,and in this Review we hereafter refer to these as replica-tion-coupled histones.Each of the replication-coupled histones is encoded by multiple genes and,with a few exceptions,most of these genes are organized into clusters throughout the genome4,5(FIG.1a).This prob-ably ensures that the expression of replication-coupled histones,which takes place during S-phase,generates large and equal amounts of all four nucleosome core histone proteins,thereby providing a constant source of nucleosomes at newly replicated DNA strands and allowing efficient chromatin packaging.By contrast,histone variants are typically encoded by a single gene(as in the case of H2A.X6)ortwo genes(in the cases of H3.3,H2A.Z and macroH2A).These genes are located outside the replication-coupled histone clusters that are present on other chromosomes,providing the possibil-ity of variant-specific transcription and deposition throughout the cell cycle.Whereas most histone vari-ants are expressed in somatic tissues,some are exclu-sively or predominantly found in the male germline7.Insummary,each histone variant has a unique temporal expression and,as we discuss below,this unique expres-sion pattern accounts for specific cellular functions of the variants.1Josep Carreras Leukaemia Research Institute,Campus Institut Catal dOncologia Germans Trias i Pujol,Campus Can Ruti,08916Badalona,Spain.2Program for Predictive and Personalized Medicine of Cancer,Germans Trias i Pujol Research Institute,08916Badalona,Spain.3Center for Integrated Protein Science Munich and Department of Molecular Biology,BioMedical Center,Ludwig-Maximilians University Munich,82152Planegg-Martinsried,Germany.4Present address:Institute forGenetics,Justus Liebig University Giessen,35392Giessen,Germany.mbuschbeckcarrerasresearch.org;sandra.hake gen.bio.uni-giessen.dedoi:10.1038/nrm.2016.166Published online 1 Feb 2017Variants of core histones and their roles in cell fate decisions,development and cancer Marcus Buschbeck1,2 and Sandra B.Hake3,4Abstract|Histone variants endow chromatin with unique properties and show a specific genomicdistribution that is regulated by specific deposition and removal machineries.These variants inparticular,H2A.Z,macroH2A and H3.3 have important roles in early embryonic development,and they regulate the lineage commitment of stem cells,as well as the converse process of somatic cell reprogramming to pluripotency.Recent progress has also shed light onhow mutations,transcriptional deregulation and changes in the deposition machineries of histone variants affect the process of tumorigenesis.These alterations promote or even drive cancer development through mechanisms that involve changes in epigenetic plasticity,genomicstability and senescence,and by activating and sustaining cancer-promoting gene expression programmes.REVIEWSNATURE REVIEWS|MOLECULAR CELL BIOLOGY VOLUME 18|MAY 2017|299 2017 Macmillan Publishers Limited,part of Springer Nature.All rights reserved.UrochordatesAlso called tunicates.Small marine invertebrates that exhibit a simplified chordate body plan and are within the chordate phylum,which includes the closest relatives ofvertebrates.PseudogenesGenes and gene copies that have lost their protein-coding function.Replication-coupled and variant histone-encoding RNAs differ in their structure and processing.Replication-coupled histone genes lack introns and contain a speci-fic 40 bp sequence downstream of the translation stop codon that forms a consensus stem loop structure that is responsible for the processing of the 3 ends8.By con-trast,several histone variant genes,albeit not all,contain introns that need to be spliced during RNA processing,which provides the chance to generate alternative splice isoforms and,in turn,to further increase histone diver-sity and also in the case of core histones nucleosome diversity9.Examples of core histone variant proteins generated by alternative splicing are macroH2A1.1 and macroH2A1.2(REF.10),as well as H2A.Z.2.1 and the primate-specific H2A.Z.2.2(REF.11).In addition,similarly to most cellular mRNAs,most histone variant mRNAs have a poly(A)tail12.At the protein level,all replication-coupled and variant histones differ in their primary sequences,and sometimes in their secondary and tertiary conformations.In some cases for example,for the replication-coupled H3.2 and the histone variant H3.3 they differ in only a few amino acids,whereas other variants such as those in the H2A family can have largely distinct sequence stretches or even unique domains(FIG.1b).This Review focuses on mammalian core histone vari-ants.We briefly discuss how these histones are deposited on DNA,and how they affect chromatin and its func-tions.However,we devote the majority of this article to outlining the normal functions of histone vari ants in development and their pathophysiological roles in cancer.The evolution of histone variants,their roles in environ-mental responses and their biochemical regulation have been comprehensively reviewed elsewhere1317.Deposition and chromatin occupancyReplication-coupled and variant core histone proteins differ not only in their temporal expression pattern but also in their spatial localization,both in the 3D nuclear space and in their distribution along the linear genome.Replication-coupled histone proteins are distributed rather equally in chromatin,whereas histone variant-containing nucleosomes show specific and unique distrib utions.Generally,nucleosomes are generated when 147 bp of DNA are wrapped around an octamer of histones that is formed of an(H3H4)2 tetramer and two dimers of H2AH2B,which are packaged on either side18.To ensure spatially and temporally controlled histone deposition and eviction,which are necessary to modulate chromatin organization and consequently Nature Reviews|Molecular Cell BiologyH2AH2BH3H2AH2BH3H4H2AH2BH3H4H2AH2BH3 H4H2AH2BTSH2BH2A.X83.8%H2A.Z.158.3%H3.1CENP-A45.1%H3.2H3.Y77.8%H3.1t97.0%H3.593.3%99.3%H3.3H3.X73.3%96.3%H2A.Z.2.159.1%H2A.Z.2.254.5%macroH2A1.162.0%macroH2A1.262.0%macroH2A260.5%H2A.Bbd38.1%84.9%H2BFWT33.3%6abH2AH2BH3H4Replication-coupled histonesFigure 1|Comparing replication-coupled and variant human core histones.a|Whereas individual genes encode histone variants,at least in humans,replication-coupled histones are encoded by multiple gene copies(each gene is represented by a coloured square in the top right panel)that are present in clusters(lower right panel)on different human chromosomes.Note the presence of several different clusters of histone genes in one chromosomal region.No distinction between genes and pseudogenes has been made in this figure.Chromosome 6 is shown here,as it harbours the largest cluster of histone genes.b|A depiction of human variants of histone H2A(yellow),H2B(orange)and H3(blue),with variants shown in pale yellow,pale orange and pale blue,respectively.Rectangles represent core regions,and lines represent flexible histone tails.No variants of H4(green)have yet been discovered in humans.Testis-specific histone variants are highlighted by light purple boxes,and alternative splice isoforms by light green boxes.Percentages indicate total amino acid sequence conservation(%sequence identity)of the variants relative to their replication-coupled counterparts(for H3,two replication-coupled isoforms are present(H3.1 and H3.2);in the figure,sequence conservationwas calculated for H3.1).CENP-A,histone H3-like centromeric protein A;H2BFWT,histone H2B type WT;TSH2B,testis-specific histone H2B.Part a is adapted with permission from REF.4,Springer.REVIEWS300|MAY 2017|VOLUME 18 2017 Macmillan Publishers Limited,part of Springer Nature.All rights reserved.Histone chaperonesHistone-binding proteins that facilitate histone-dependent processes,including histone deposition on and removal from chromatin.Chromatin remodellersFrequently multimeric complexes that use ATP to catalyse changes in chromatin structure,including the exchange of histones.DNAtemplate-based processes biological functions,speci fic chaperone and ATP-dependent remodel-ling complexes have evolved19(FIG.2a;TABLE1).Histone chaperones participate in multiple steps of nucleosome formation20 and bind histones directly after their syn-thesis to control their stability or degradation21.Some chaperones assist in the cytoplasmnucleus trafficking of histones directly after their synthesis,in part through regulating their interaction with importins22;others affect histone post-translational modifications(PTMs)by facilitating the binding of histones to the responsible enzyme8;and others facilitate histone interactions to pro-mote nucleosome formation23,24.By contrast,chromatin remodellers use ATP to organize chromatin structure by sliding or ejecting assembled nucleosomes and,impor-tantly,can allow the exchange of labile H2AH2B dimers with dimers of histone variants25.One of the first histone variant-specific chaperone complexes to be discovered was theH3.3-specific histone cell cycle regulation-defective homologue A(HIRA).Aspart of a separate complex,chromatin assembly factor1(CAF1;also known as CNOT7)is involved in H3.1 and H3.2 deposition during replication,which reveals the existence of distinct deposition machiner-ies and pathways responsible for DNA synthesis-independent and DNA synthesis-dependent chroma-tin assembly24.Later,another H3.3-specific depo sition complex namely,the death domain-associated pro-tein 6(DAXX)ATRX complex was identified26.Both the HIRA complex and the DAXXATRX complex have non-redundant roles in the deposition of H3.3 in differ-ent chromatin environments and have different func-tional outcomes26.Whereas HIRA-deposited H3.3 at sites of naked DNA,such as regions of gene activation,might Homotypic nucleosomeNucleosomestructure andstability changeHeterotypic nucleosomePTM changes Due to amino acid sequence Due to chromatin environmentChanges to the histone codeand its read-outIndirect effects of histone variant depositionDirect effects of histone variant depositionbaH2A variantH2BHistonechaperonesStabilization offree histonesNuclear importRibosomeHistone chaperoneand chromatin-remodelling complexHistoneexchangeNucleosomeassembly anddepositionChange innucleosomeoccupancyOpen versusclosed chromatinPTM readerVariant-specificreaderH2A variantsReplication-coupled H2AH3 variantTrimethylationDNAFigure 2|The roles of histone chaperones and remodellers,and the impact of histone variants on chromatin.a|Specific histone chaperone and chromatin-remodelling complexes recognize histone variants when they are complexed with their replication-coupled partner histone(after synthesis,the H2A variant shown here(pale yellow)pairs with H2B(orange),whereas H3 pairs with H4(not shown).Chaperones stabilize histones and prevent their degradation.They also have a role in the nuclear import of histones and facilitate histone exchange,as well as nucleosome assembly and deposition.ATP-dependent chromatin-remodelling enzymes slide nucleosomes on DNA or allow the exchange of labile H2AH2B dimers with dimers that contain an H2A variant.b|The incorporation of histone variants(pale yellow andpale blue)into chromatin can result in homotypic or heterotypic nucleosomes(top)and can have direct(middle)orindirect(bottom)effects on chromatin structure and function.Histone variants can directly influence nucleosome structure and stability,thus resulting in changes in the local chromatin environment(for example,they can affect the propensity for chromatin remodelling).The composition of the nucleosome can also have indirect effects on chromatin organization and function.The presence of histone variants can induce the recruitment of specific readers of histone post-translational modifications(PTMs)and/or the recruitment of variant-specific binding complexes,which can then induce local chromatin changes.REVIEWSNATURE REVIEWS|MOLECULAR CELL BIOLOGY VOLUME 18|MAY 2017|301 2017 Macmillan Publishers Limited,part of Springer Nature.All rights reserved.Table 1|Histone variants and their regulation by histone chaperones and chromatin remodellersHistone or variantTissues(location within thegenome)Chaperones and remodellersFunctionRefsH2A*H2B*complexAll(genome-wide)FACT(chaperone)Deposition and exchange of histones167NAP1(chaperone)Nuclear import and deposition168,169Nucleolin(chaperone)Deposition and exchange of histones170H2A.XAll(genome-wide)FACT(chaperone)Deposition and exchange of histones167H2A.Z.1All(regulatory regions(promoters and enhancers)andheterochromatin)p400(remodeller)H2A.Z deposition11SRCAP(remodeller)H2A.Z deposition11ANP32E(chaperone)H2A.Z chromatin removal at sites of DNAdamage3537INO80(remodeller)H2A.Z removal,which promotes homologous recombination171H2A.Z.2.1All(regulatory regions(promoters and enhancers)andheterochromatin)p400(remodeller)H2A.Z deposition11SRCAP(remodeller)H2A.Z deposition11H2A.Z.2.2All but enriched in the brainp400(remodeller)H2A.Z deposition11SRCAP(remodeller)H2A.Z deposition11MacroH2A1.1All(facultative and constitutive heterochromatin)Not knownNot knownMacroH2A1.2All(facultative and constitutive heterochromatin)ATRX(remodeller)Negative regulation,possibly indirect33